TGAC ISPG - Developing Strategies for Big Data Bioinformatics

Abstract

This ISP proposal aims to develop bioinformatics tools to handle and process big genomics datasets. DNA sequencing has become an enabling technology at the heart of a revolution in life sciences. The objectives in this proposal focused on providing in the next 5 years the tools required to realise the value of big data bioinformatics. The mission of TGAC is to establish a centre of scientific excellence specialising in genomics technology, high throughput data generation and bioinformatics to work along side the UK scientific community around the BBSRC strategic research priorities for 2010-2015: food security, bioenergy and biology underpinning health. The implementation of this ISP will set up the foundations to fully develop the incipient bioinformatics groups at TGAC into a World-class research centre. The objectives for this proposal are organised in three themes: the processing of raw data into genomic information, the translation of this information into biological knowledge, and the development of an infrastructure to sustain these activities. The demands in terms of volume and data types are varied and require different skills sets and emphasis. The first objectives focus on the processing of large datasets with two concrete examples of application in genomics that are relevant to the BBSRC research community. The development of efficient assembly algorithms for large eukaryote genomes from short reads is still a topic of intensive research. In fact the product obtained from the high-throughout sequencing technologies although much cheaper is of lower quality than the assemblies generated by the previous technologies. This is a challenge that will particularly affect the development of genomics research for plant with complex and large genomes characterised by other features such as polyploidy and nested repeat structures that complicate the assembly process.

We have developed and implemented enhanced protocols for sequencing in a cost-effective way. We have developed ability to generate sequence assemblies with increased contiguity and correct representation on heterozygous assemblies of complex crop species and pathogens. We have developed a data management and federation platform to enable researchers to gain easier access to large wheat datasets and analytical pathways capable of dealing with them. We deployed improved data tracking and analysis systems though platforms such as Cyverse UK, Galaxy and COPO. We have developed methods to identify variants in several species with complex genomes with a focus on induced variation (exome captures for bread wheat, barley and brassica) and diversity sets (e.g. rice, barley, ash tree and willow). we have developed tools for assembling and representing variation in viral metagenomics and to identify microbial and eucaryotic species using new sequencing technologies. Finally we have developed We have developed laboratory protocols and annotation approaches to improve the coding and non-coding annotation of complex crop species.

Exploitation Route

The new methods and novel strategies developed for the application of high throughput sequencing technologies to plant, and animal health deliver have had direct impact on the the academic and industrial communities centered around the three BBSRC scientific priorities: food security, bioenegry and biology underpinning health. We have facilitated the access to complex crop genomes such as the wheat sequence and we have provided convenient and user-friendly tools to access the genomic features will have a direct impact on the way research is conducted on cereals and other food crops. We have generated and made accessible a wealth of information that breeders can use to rapidly select for varieties with favourable traits, and also for plant scientists to conduct basic research on crops. We have established long lasting partnerships with the UK and international scientific community, successfully implementing our developed strategies through collaborations and by providing training in emerging technologies and bioinformatics and access to data analysis platforms.

By improving the performance and capacity of assembly algorithms we have facilitated the access to complex crop genomes such as the wheat sequence by breeders, agri-tech industries and producers. Through the work in the work within the existing NC in Genomics we have established processes to address global food security concerns through responding to plant pathogen outbreaks worldwide e.g. ash dieback, yellow rust, wheat blast.

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to study chromatin accessibility. Having first been described in 2013, it has not been extensively applied to teleost fish model systems, including cichlids.

Type Of Material

Technology assay or reagent

Year Produced

2017

Provided To Others?

No

Impact

We worked towards developing the technique to study chromatin accessibility in cichlid tissues, enabling an added angle of epigentic study contributing towards speciation/adaptation events in these fish. As such, collaborators are now interested in including the approach to study cichlids in future grants and we have also included in current Core-Strategic Programme grants. Also, we plan to roll the technique out as a service for sequencing platform users.

Title

Plant R genes pipeline

Description

A set of scripts for identification of plant NLR immune receptors, including non-canonical domain architectures.

Type Of Material

Technology assay or reagent

Year Produced

2016

Provided To Others?

Yes

Impact

We have used this tool to annotate plant immune receptors in over 150 plant genomes. This tool has been used by multiple other academic groups. Our open access publication (Sarris et al BMC Biology 2016) that originally described our approach and initial results has been cited 47 times, accessed 9,363 times and has an Almetric attention score of 103. It has been mentioned in 7 news outlets, 3 blogs and 52 tweeters.

A manually curated dataset of autophagy components and their interactions.
Integrated resource with known protein regulators of autophagy.
Contains possible transcriptional and post-transcriptional regulators (ie., transcription factors and miRNA) of autophagy and its protein regulators.
Links all autophagy component and regulators to major signaling pathways.
Predict novel regulators and interactions.
Can be downloaded in a user-specified content and format.

A manually curated dataset of regulatory connections of NRF2
Integrated resource with known protein regulators of NRF2
Contains possible transcriptional and post-transcriptional regulators (ie., transcription factors and miRNA) of NRF2 and its protein regulators.
Links NRF2 and regulators to major signaling pathways.
Predict novel regulators and interactions.
Can be downloaded in a user-specified content and format.

Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. Lack of recombination limits breeding efforts in crops, therefore increasing recombination rates can reduce linkage-drag and generate new genetic combinations. We use computational analysis of open access data from 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We find that high frequency crossover sites are shared between populations and that closely related parental founders lead to populations with more similar crossover patterns. We have identified QTL for altered gene conversion and crossover frequency and confirm functionality for a novel candidate RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages. Harnessing the RecQ helicase has the potential to break linkage-drag utilizing widespread gene conversions conserved across recombination sparse centromeric regions.

An integrated network resource containing regulatory, metabolic and protein-protein interactions
For multiple Salmonella strains classified as gastro-intestinal or extra-intestinal pathogens
An interaction resource with manually curated, high-throughput and predicted interactions
Provides a strain specific and consensus networks
Can be downloaded in a user-specified content and format

Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes.
We present Aequatus, a standalone web-based tool that provides an indepth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow.
Aequatus is an open-source tool freely available to download under the MIT license at https://github.com/TGAC/Aequatus. A demo server is available at http://aequatus.earlham.ac.uk/. A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server at https://usegalaxy.eu

Type Of Material

Database/Collection of data

Year Produced

2018

Provided To Others?

Yes

Description

BRIDGE Colombia Network

Organisation

Aberystwyth University

Department

Institute of Biological, Environmental and Rural Sciences (IBERS)

Country

United Kingdom

Sector

Academic/University

PI Contribution

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute founded the BRIDGE Colombia network of Colombia, British and International organisations following the success of an IAA funded workshop around Colombian Biodiversity. The development of the BRIDGE day 2017 and 2018. In 2018 it was decide that GROW and BRIDGE would aligned with some projects of the Newton Caldas programme

Collaborator Contribution

The network is a multidisciplinary network of researchers and organisations with an interest in preserving Colombian biodiversity and promoting the sustainable use of natural resources. Each network partner has contributed to ongoing discussions about current and future research proposals and ideas.

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity

Collaborator Contribution

The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products

This project aims to leverage these new resources together with large gene expression data sets to reconstruct regulatory networks controlling important traits. With outputs feeding directly into UK and International wheat research and UK wheat breeding programmes. The collaboration focuses around two large data sets: the first, a high resolution time series data set for wheat and the second, a developmental time course for 16 international elite cultivars.
The project aims to:
1. Develop normalisation methods for the transcriptome data sets (RNA-seq data), specific for dealing with the complexities of time course data and a complex polyploid genome. Benchmark these new approaches against existing tools.
2. Develop AI pattern matching algorithms to identify gene-expression modules and correlate these with biological processes. Use pattern matching algorithms to interrogate the high resolution data sets and to identify differences between regulatory networks in elite cultivars
3. Correlate changes in temporal or developmental expression patterns with changes in promoter architecture
4. Use network inference, co-expression and gene modules to reconstruct regulatory networks. Identify how network structure changes over time and between cultivars.
This project will have impact for scientists as it will address fundamental questions about temporal regulation of processes in wheat and how a complex networks work across multiple genomes within a polyploid. By comparing networks across elite cultivars it will also have an impact for UK and international wheat breeders, identification of how breeding programmes have changed the architure of regulatory networks. This will have important impact for the selection of future networks for breeders to target or for assessing the selection of breeding material. It will allow breeders to make full use of the new resources and technologies. To ensure the impact to the UK industry is realised we aim to present this work a UK networking meeting and to visit and involve three private UK breeding companies RAGT, KWS and Elsoms seeds in early output from the project.

Collaborator Contribution

IBM have are involved in applying ML and AI approaches to analyse gene expression data in wheat and reconstruct gene networks.

Impact

No outputs to data

Start Year

2017

Description

KWS

Organisation

KWS UK

Country

United Kingdom

Sector

Private

PI Contribution

Generated double haploid population for the IWYP project and provide material for INTREPID and the BBSRC/EAGER work

Collaborator Contribution

Know of the techniques and approaches we are using, early access to the data we generate

Impact

Double haploid seed population

Start Year

2017

Description

RGB-Net: a Collaborative European Network on Rabbit Genome Biology

Organisation

University of Bologna

Country

Italy

Sector

Academic/University

PI Contribution

The COST action brings together experts in all rabbit research areas and in other complementary research fields (breeders, geneticists, bioinformaticians, physiologists, evolutionists, embryologists, immunologists, industry experts, etc.) in order to facilitate the transition of rabbit genomic information from experimental data into usable benefits and applications by means of networking expertise. Federica Di Palma contributes towards one of four Working Groups.

Collaborator Contribution

The four working groups focus on i) the refinement of the European rabbit genome resource and the development of genome-based platforms, ii) genetic aspects in meat, fur and pet rabbits and biodiversity resources, iii) the rabbit as a model in basic biology and human diseases and as a tool for biotechnology applications and iv) genetic and comparative genomic aspects for the study, exploitation and management of wild lagomorphs. The outcome is a coordination of rabbit research activities and a transfer of knowledge which will produce a strong European added value across a broad spectrum of biology research fields

Impact

Conference poster and talks

Start Year

2013

Description

Wheat Information System (WheatIS)

Organisation

Cold Spring Harbor Laboratory (CSHL)

Country

United States

Sector

Charity/Non Profit

PI Contribution

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative.

Collaborator Contribution

All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project.

We provided the sequence data. Both groups undertook assembly strategies that were published alongside each other

Collaborator Contribution

The Helmholtzz group provide annotation and analysis which were published in the paper.

Impact

Joint grants including ERA-CAPs BBSRC grant. Co publication of the wheat methylome. Ongoing collaboration through the wheat genomics community on annotation and analysis

Start Year

2011

Title

Aequatus

Description

Aequatus Browser is an open-source web-based tool developed at EI to visualise homologous gene structures among differing species or subtypes of a common species. Aequatus uses the Ensembl Compara and Core database schemas to store comparative information between organisms.
Aequatus uses precalculated gene family information and genomic alignments data in the form of CIGAR strings, from Ensembl Compara or the GeneSeqToFamily pipeline, and cross-references these sequences to Ensembl Core databases for each species to gather genomic feature information via stable_ids. Aequatus then processes the comparative and feature data to provide a visual representation of the phylogenetic and structural relationships among the set of chosen species.
The ultimate goal of the Aequatus Browser is to provide a unique and informative way to render and explore complex relationships between genes from various species at a level that has so far been unrealised.

COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories. COPO facilitates the links to data analysis platforms such as CyVerse UK and Galaxy. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces. This improvement output represents the beta release of the COPO platform in 2017.

Type Of Technology

Webtool/Application

Year Produced

2017

Open Source License?

Yes

Impact

COPO has been added to the ELIXIR-UK roadmap for ELIXIR core data services, and is currently being used by EI and JIC researchers to deposit real, large scale sequencing datasets into the European Nucleotide Archive. COPO is also being investigated as a potential data entry tool for the CGIAR Big Data project, and this will be explored in a joint EAGER submission with CIMMYT. COPO has also been selected to act as one of the data ingestion pipelines for data arising from the Designing Future Wheat programme, depositing open data into the Grassroots repository. COPO is also being included in grant submissions to assist vertebrate and wheat communities in effective metadata management. COPO runs within the CyVerse UK National Capability infrastructure.

COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories and to facilitate links to data analysis platforms. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces.

Type Of Technology

Webtool/Application

Year Produced

2015

Impact

The software is in an early stage, but functional for deposition of data to a small number of repositories. As such we are not yet ready for end-user testing.
However, we are collaborating with Cyverse US (was iPlant Collaborative) to investigate the use of COPO as the brokering system for their Data Commons.

The CyVerse (formerly iPlant) UK project at EI provides hardware resources in an easy to use manner through a web interface called the Discovery Environment (DE), as well as developer and bioinformatician access through APIs and software. A series of commands, called a pipeline, is combined into a script and / or a virtualised operating system container image called Docker. The pipeline can run on any hardware available to the implementer, which in this case will be the extensive HTCondor cluster set up at EI. Once a pipeline is running correctly on through the raw scheduler, the app can be registered on the Agave API (http://www.agaveapi.co). This is enabled through constructing JSON files that specify input sources together with user-supplied and default parameters that are necessary for the pipeline to run. Once a pipeline is registered through Agave, it is available as a GUI "app" through the DE, and can be made public after testing.

Type Of Technology

Grid Application

Year Produced

2016

Impact

The EI CyVerse hardware enables the bioinformatics pipelines developed by the project partners (Univ's. Liverpool, Nottingham, Warwick) to be run on this HPC environment. Once deployed in the CyVerse UK environment, these tools can then be made available globally through the CyVerse Discovery Environment, reaching upwards of 18000 potential users.
We have released this infrastructure and are accepting users from the UK research community to start using the hardware.

GeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy's user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

Type Of Technology

Software

Year Produced

2017

Open Source License?

Yes

Impact

This new workflow has been used for a number of research projects at the Earlham Institute, including the investigation of gene families for the koala genome, in collaboration with Kathy Belov, Wilfried Haerty, Will Nash and Federica di Palma. The workflow was published as a preprint on bioRxiv in 2017 and subsequently accepted into the GigaScience journal in 2018.

Title

Grassroots API

Description

The Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected.
With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box.

Type Of Technology

Software

Year Produced

2015

Open Source License?

Yes

Impact

The Grassroots API powers the public BLAST service that runs at TGAC, predominantly for the currently available wheat assemblies including the recently released TGAC v1 w2rap assembly (in preparation). We have served over 4000 unique users with over 6000 BLAST jobs since November 2015.
It also underpins the Field Pathgenomics project (BBSRC IPA award 2015, PI - Saunders D., TGAC/JIC fellow), a web portal that represents the detection and subsequent phenotyping and genotyping of the wheat yellow rust pathogen. The site aims to enable researchers and breeders to track rust epidemics over variety and time, allowing for a more proactive approach to wheat crop breeding and farming.
Finally, we are working with the CerealsDB group at Univ. Bristol to deploy the Grassroots infrastructure alongside the CerealsDB web portal, allowing a federation of searching, datasets, analysis and dissemination of markers, genotypes and associated feature and literature information.

KAT is a tool to perform kmer-spectra analyses. Arguably the most widely used feature is the comparison of the kmer spectra of a short-read dataset and a genome assembly for the same individual (often created from this same dataset). It highlights deviations and biases in sample-reconstruction, providing means for QC. Among the crucial information easily accessible is whether all of the sequenced content is included in the assembly and if there are compressed or expanded regions: these are metrics directly related to the usability of the assembly for biological research.

Type Of Technology

Software

Year Produced

2013

Open Source License?

Yes

Impact

The insight from KAT spectra comparisons is widely appreciated within the genome assembly community and underpins a great deal of work in genome assembly at EI.

MISO (Managing Information for Sequencing Operations) is an open-source Lab Information Management System (LIMS) started at the Earlham Institute, specifically designed for tracking next-generation sequencing experiments.
Sequencing centres differ not only in terms of their scale and output, but also their requirements for information management. Sequencing platforms are becoming more accessible, and the efficient storage of genomic metadata is vital for large and small sequencing centres alike. Off-the-shelf solutions are often very expensive and not cost-effective for the smaller centre. Furthermore, support contracts are often required, and the extensibility of these systems is not in the hands of the metadata generators. In terms of implementation, as well as the desire to tailor an information system in-house, data formats can change and platforms can evolve rapidly. These are valid concerns for both large centres characterised by high-throughout data production and smaller scale laboratories with constrained expenditure for IT solutions, and potentially project specific metadata requirements.
Hence, we are developing MISO, an open-source LIMS for recording sequencing metadata. We are using freely available tools that are industry standard, well documented, and easy to set up on minimal hardware. As a bare system, MISO can store relevant metadata based on a wide array of NGS sequencing platforms (e.g. Illumina GA, HiSeq and MiSeq, Roche 454, ABI SOLiD and PacBio RS) and public repository data submission schemas (e.g. the Sequence Read Archive at the EBI), and has many features common to bespoke and proprietary LIMS, such as secure authentication, fine-grained access control, barcode tracking, and reporting.

Type Of Technology

Webtool/Application

Year Produced

2018

Open Source License?

Yes

Impact

A number of new MISO releases have been made available this year, the latest being 0.2.109. The project has seen over 140 releases in its 7 year existence, and the project is 100% open source, allowing sequencing centres to have the option of a completely free solution for managing their instruments and sample tracking.

MetaCortex is an assembly tool for metagenomic sequence data. We are preparing a paper for publication, but the software is available already.

Type Of Technology

Software

Year Produced

2017

Open Source License?

Yes

Impact

A number of research groups are already using the software.

Title

Nextclip

Description

NextClip is a tool for comprehensive quality analysis and read preparation for Nextera long mate pair (LMP) libraries. NextClip comprises two parts. The core component is the NextClip command line tool, an efficient C program for processing mate pair FASTQ files, generating summary statistics and preparing reads for use in scaffolding. A second component, the NextClip pipeline, is designed for cases where there is a reference of partially assembly. It utilises NextClip, along with BWA, to generate a more detailed PDF report that includes analysis of library insert sizes. The tool was originally described in a publication in Bioinformatics (2014), but has since been updated, e.g. the addition of an option for deduplicating reads from any library type.

Type Of Technology

Software

Year Produced

2014

Open Source License?

Yes

Impact

Many users around the world who are using it do improve data quality and downstream analysis.

The Grassroots software is an open source "as-a-Service" stack that powers a number of data dissemination and analysis activities at EI, and other sites such as CerealsDB at the University of Bristol. We have continued to develop the functionality within the software stack to share crop-related datasets.

Type Of Technology

Webtool/Application

Year Produced

2018

Open Source License?

Yes

Impact

Grassroots has previously been used to host the Field Pathogenomics project website and Yellow Rust map, the EI wheat BLAST service, the CerealsDB federation project, and the multi-scale improvements to the Polymarker marker design software. Recently, Grassroots has been put forward as the main data repository and metadata catalogue for the Designing Future Wheat project, and has started to host data from this project, the Open Wild Wheat Consortium, and 5 new wheat genomes from EI. The Grassroots service runs within the CyVerse UK National Capability infrastructure.

w2rap is a genome assembly pipeline for complex genomes from short reads.

Type Of Technology

Software

Year Produced

2017

Open Source License?

Yes

Impact

W2rap has enabled wheat genomics to jump into a new era of high-quality genomes from short reads. While there are some alternative tools from private companies, w2rap remains the standard for quality reconstruction across the genome. W2rap has already been used to assemble 5 wheat genomes in the public domain, putting the UK at the forefront of wheat genomics. With tens of genomes being assembled now, new modules veing developed for new data types, and 5 wheat lines assembled in a £1M private project, w2rap is one of the flagship projects for Earlham Institute.

Evolutionary History and Domestication of the Ferret (Mustela putorius furo). Genome Science 2016

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The domestic ferret (Mustela putorius furo) models biological processes that are highly relevant to human disease and health research such as influenza, cystic fibrosis and asthma. The recently completed draft of the ferret genome and associated annotation project (Peng et al 2014) allows us to extend research and examine the domestication of the ferret. Most domestic animals were domesticated ~10,000 years ago, but the history of the ferret's domestication is uncertain. It is likely that ferrets have been domesticated for at least 2,000 years, a similar time to the domestication of the rabbit, of which the ferret was domesticated to hunt. We have sequenced the genomes of a further eight domestic ferrets along with 12 European Polecats (M. putorius), 2 Steppe Polecats (M. eversmanii) and 4 Black-footed Ferrets (M. nigripes). In order to examine the genetics underpinning ferret domestication and compare the genomes of domestic and wild ancestor, we first need to identify the ancestral species of the domestic ferret, the identification of which is not fully resolved.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

UK scientists have identified the country's first ash tree that shows tolerance to ash dieback, raising the possibility of using selective breeding to develop strains of trees that are tolerant to the disease. SOCIAL MEDIA Engagement 75 Impressions 98,100

We put on lots of different activities to celebrate Ada Lovelace Day, including written pieces for the website, a cryptic crossword of women in science, as well as bake sales and more. The event was publicised across campus, even attracting members of the public to come to the research park on the day in question.

Workshop to look at: Genetic improvement in aquaculture and its impact around the world by WorldFish; Aquaculture development in Africa: the case of Malawi by WorldFish (Malawi); Tilapia and its endemism in Africa: challenges and opportunities; Experiences of small scale fish farmers in Tanzania: case studies by TAFIRI; Aquaculture Policy in Tanzania by Director of Aquaculture Tanzania; Aquaculture research and technology transfer; Potential species/strains for breeding program in Tanzania; Aquaculture entrepreneur-researcher interaction in Tanzania: challenges and opportunities by SUA; The status of aquaculture breeding programs in Africa and lessons from Malaysia by UDSM; Tilapia aquaculture development strategy in Tanzania and possible collaborations (Remarks on way forward from TAFIRI, UDSM, SUA, Bangor, Earlham, SLU, WorldFish, Aquaculture Department -MALF)

Year(s) Of Engagement Activity

2016

Description

Aphids - the versatile agricultural nuisance

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

At EI, we research pests such as aphids, to better inform us of the versatile evolutionary strategies that help them ravage our crops, and how we can combat their game plan.

I became fascinated with aphids when, after bringing a chive plant in from the cold, a ravenous horde descended upon our carnivorous sundew plant. SOCIAL MEDIA 118 Impressions 186135

Overfishing has been rife for decades and our seas and oceans have become vastly depleted in fish reserves. Despite this, over 70% of the world's population lives on the coast, relying on fish as a major protein source. It is time to look inland, towards freshwater aquaculture. SOCIAL MEDIA Engagement 62 Impressions 91764

Article to highlight the research on EUropean polecat - Unseen in areas for more than a hundred years, the European Polecat (Mustela putorius) has recolonised over extensive parts of the UK. Recently hitting the news headlines, the native British species of the mustelid family is back. SOCIAL MEDIA Engagement 54 Impressions 57,200

In November 2015, TGAC teamed up with Thought for Food in order to put on a workshop for WIRED2015: Next Generation on the subject of biohacking, and how we might use it to feed nine billion mouths by 2050.

Over two workshops, attended by young people aged 12-18 (along with some parents), participants were given an introduction to the potential of modern genome sequencing and how we can use the wealth of information gleaned from it in order to better understand, and improve our food.

The attendees were enthused and inspired about the topic of food security and how modern techniques mean that DNA sequencing can be performed cheaper and faster than ever before. SOCIAL MEDIA Engagement 169 Impressions 86600

Article to promote our broad research interests - Our diverse projects covering the breadth of life on earth are helping us to improve human, animal and plant health, while aiding in researching healthier living systems. SOCIAL MEDIA Engagement 13 Impressions 21,600

Web article - At EI, we recently heard from Dr Anthony West - automation specialist in our Platforms & Pipelines group - who filled us in on the power and technical difficulties of a new approach to biotechnology: Synthetic Biology. SOCIAL MEDIA - Engagement 75 Impressions 84,400

Article - Two such tools developed at Earlham Institute in the Swarbreck Group have paved the way to drastically enhance how we can do this: Portcullis, developed by Daniel Mapleson, and Mikado, developed by Luca Venturini, have recently been released to the public, and are available for any scientist who wants to accurately identify important regions within genomes. SOCIAL MEDIA Engagement 95 Impressions 100,000

Aiming to reach new heights with its bioinformatics tools for signalling networks and large-scale integrated analysis, SignaLink and NavigOmix, the Korcsmaros Group has a new addition. Aidan Budd tells us how he got into building successful scientific communities and his new role at EI - with caffeine proven as a key contributor! SOCIAL MEDIA Engagement 135 Impressions 140,000

Highlighting the research and studies of the Hen Harriers - We speak to our conservation genomics expert Dr Graham Etherington on how the Hen Harrier is actually two species rather than one - correct classification will help save these endangered birds of prey.. SOCIAL MEDIA Engagement 29 Impressions 46,800

To celebrate Ada Lovelace Day, we asked staff on Norwich Research Park to tell us of their inspirational role models in STEM, and how they inspired them to pursue a science career. A video and written article was produced. SOCIAL MEDIA Engagement 101 Impressions 90,800.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

The third edition of "Guidelines for the use and interpretation of assays for monitoring autophagy" was recently published in the leading journal Autophagy, featuring the Earlham Institute's (EI) Autophagy Regulatory Network resource and co-authored by Dr Tamas Korcsmaros, Computational Biology Fellow at EI and Institute of Food Research (IFR).

Over 40 delegates from Colombia and the UK attended the EI led workshop. Attendees discussed ideas and plans for research involving the management, conservation, and use of Colombian natural resources. The workshop led to the development of the BRIDGE Colombia network of researchers and raised the international profile of EI, particularly in Latin America.

BROADCAST: The Genome Analysis Centre announces an important milestone in wheat research

Form Of Engagement Activity

A broadcast e.g. TV/radio/film/podcast (other than news/press)

Part Of Official Scheme?

No

Geographic Reach

Local

Primary Audience

Public/other audiences

Results and Impact

06:34, BBC Radio Norfolk - Wheat

Year(s) Of Engagement Activity

2015

Description

BROADCAST: The Genome Analysis Centre announces an important milestone in wheat research

Form Of Engagement Activity

A broadcast e.g. TV/radio/film/podcast (other than news/press)

Part Of Official Scheme?

No

Geographic Reach

Local

Primary Audience

Public/other audiences

Results and Impact

08:04, BBC Radio Norfolk - Wheat

Year(s) Of Engagement Activity

2015

Description

BROADCAST: The Genome Analysis Centre announces an important milestone in wheat research

Form Of Engagement Activity

A broadcast e.g. TV/radio/film/podcast (other than news/press)

Part Of Official Scheme?

No

Geographic Reach

Local

Primary Audience

Public/other audiences

Results and Impact

07:04, BBC Radio Norfolk - Wheat

Year(s) Of Engagement Activity

2015

Description

BROADCAST: The Genome Analysis Centre announces an important milestone in wheat research

Form Of Engagement Activity

A broadcast e.g. TV/radio/film/podcast (other than news/press)

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Public/other audiences

Results and Impact

BBC 1, Look East (Ipswich/Norwich) - Wheat

Year(s) Of Engagement Activity

2015

Description

BROADCAST: The World - The year of CRISPR: scientists celebrate new genome tool

Form Of Engagement Activity

A broadcast e.g. TV/radio/film/podcast (other than news/press)

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Public/other audiences

Results and Impact

ABC News (Australia)

Year(s) Of Engagement Activity

2017

Description

Big Bang Fair

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Public/other audiences

Results and Impact

We trialled a game developed for public engagement, "TGAC4kids," prior to releasing a beta test version to take on our roadshow to schools.

Year(s) Of Engagement Activity

2014

Description

Big Data in Agri-tech Special Interest Group

Form Of Engagement Activity

A formal working group, expert panel or dialogue

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Industry/Business

Results and Impact

An Agri-tech East Special Interest Group on the topic of big data, and the basic advantages and challenges of adopting and using the data effectively. Networking opportunity for the KEC team to understand issues relevant to farmers, seed companies and other Agri-tech stakeholders. Gained contacts and created a link with Agri-tech East which has resulted in co-facilitated events.

In November 2015, TGAC teamed up with Thought for Food in order to put on a workshop for WIRED2015: Next Generation on the subject of biohacking, and how we might use it to feed nine billion mouths by 2050.

Over two workshops, attended by young people aged 12-18 (along with some parents), participants were given an introduction to the potential of modern genome sequencing and how we can use the wealth of information gleaned from it in order to better understand, and improve our food.

The attendees were enthused and inspired about the topic of food security and how modern techniques mean that DNA sequencing can be performed cheaper and faster than ever before. SOCIAL MEDIA Engagement 169 Impressions 86,600

Article to highlight - With our recent release of the Brassica Information Portal (BIP) - a vital, open-source tool for crop breeders and researchers worldwide - why are brassicas so brilliant, and why is the availability of BIP so important to science, agriculture, industry and us? SOCIAL MEDIA Engagement 138 Impressions 183,000

Can we produce a better wheat crop to feed the world? Single to multiple wheat genomics

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Entering a 'wheat pan-genomics' era from single to multiple wheat DNA references, the Earlham Institute (EI) aims to diversify one of the world's most complex genomes to improve yield quality and increase wider production of this critical food crop. SOCIAL MEDIA Engagement 238 Impressions 137768

Cheap and robust genomes using the PDABS pipeline Advances in Genome Biology and Technology

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

Advances in next-generation sequencing (NGS) technologies and the subsequent reduction in cost have enabled the research community to sequence the genomes of many non-model organisms. Genome assemblies using next generation technologies such as Illumina show high quality nucleotide level information, but are fragmented due to the inability to retain contiguity. The absence of low-cost methods for creating high quality genome sequences from a wide range of organisms currently hampers the generation of de novo genomes for comparative genomic studies, and new methodologies and data types need to be tested to achieve this goal. We have integrated NGS with nano-channel genome mapping and developed the PCR-free Discovar Assembly BioNano Scaffolding (PDABS) pipeline to assemble cheap, contiguous and robust genomes.

Year(s) Of Engagement Activity

2016

Description

Children of TGAC

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

Local

Primary Audience

Schools

Results and Impact

A chance for staff to show their children the research that we do, as a preamble to our "TGAC4kids" roadshow to schools. We managed to trial a lot of different activities and games before running our outreach programme throughout Norwich.

Year(s) Of Engagement Activity

2014

Description

Code for crops: Training Vietnamese Rice Breeders at EI

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

ROund up of visit to EI by researchers working on rice in Vietnam. At EI, six breeders from Hanoi learned the basics of bioinformatics, which will help them breed drought and salt resistant rice in Vietnam. Here's their story. After the success of our first trip to Vietnam to introduce 'big data' analysis to the rice breeders of the Agricultural Genetics Institute (AGI), three months on we have been delighted to host six of our collaborators and friends from Hanoi in order to teach them how to code and apply bioinformatics to their work on rice breeding (and give them a taster of an English pub lunch). SOCIAL MEDIA Engagement 56 Impressions 57,700

Over the course of the summer we hosted various colleges in order to give students an insight into what goes on in a bioinfomatics and next generation sequencing pipeline, and how this relates to applied science. Many of the students had agricultural backgrounds, therefore this fostered a good discussion on how our research is applicable beyond the research park. We also did a "Three Horizons" based activity, during which we outlined routes to a better understanding of problems and how to solve them.

Year(s) Of Engagement Activity

2016

Description

Conference Oral Presentation - Biology of Genomes, CSHL, USA

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Postgraduate students

Results and Impact

Oral presentation at the esteemed Biology of Genomes conference on Evolution of tissue-specific regulatory programs in cichlids; several questions and discussion was sparked after the presentation. Dissemination of research results enabled for wider discussion of reearch impact, future direction/studies and collaboration.

Year(s) Of Engagement Activity

2017

Description

Conference Oral Presentation - SMBE, Australia

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Postgraduate students

Results and Impact

Oral presentation at the esteemed SMBE conference on Evolution of tissue-specific regulatory programs in cichlids; several questions and discussion was sparked after the presentation. Dissemination of research results enabled for wider discussion of reearch impact, future direction/studies and collaboration.

Year(s) Of Engagement Activity

2016

Description

Conference Poster - Aquaculture Europe

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Postgraduate students

Results and Impact

Poster on Evolution of tissue-specific modular regulatory networks in tilapia and East African cichlids - enabled engagement with fellow researchers in aquaculture as well as advancement of associated technologies.

Conference poster on Evolution of tissue-specific regulatory programs in cichlids - conference attendees solely worked on the cichlid model systems and as such, we forged further collaborative research activities based on our integrative scientific approaches.

The poster presented at the International Plant and Animal Genomes Conference (San Diego, USA) conference was selected on abstract submission. The poster was presented in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Lead author Tamas Korcsmaros, Fellow at EI and the Institute of Food Research, said: "Our cells must be able to detect and respond to many different pieces of genetic information coming from both internal and external sources. However, not all proteins in the cell are equally important. SOCIAL MEDIA Engagements 121 Impressions 112,000

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

The Earlham Institute (EI) builds upon their National Capability in Genomics by adding a state-of-the-art DNA Foundry for Synthetic Biology to their world-leading advanced suite of sequencing technologies. SOCIAL MEDIA Engagement 115 Impressions 77,900

Dr Davey delivered a talk as part of the Norwich 2017 Pint of Science series about the challenges and solutions for modern data management in the life sciences, including recent data developments, high-performance computing, and software tools.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Researchers have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection that has the potential to wipe out 90% of the European ash tree population. SOCIAL MEDIA Engagement 100 Impressions 114334

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Press release to promote new HPC at EI - The Earlham Institute (EI) has announced its new partnership with Verne Global, a global-based developer at the forefront of data centre infrastructure design. SOCIAL MEDIA Engagement 47 Impressions 30,700

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Press release to promote EI being awarded bronze Athena Swan - Established in 2005, Athena SWAN recognises and encourages the careers of women in science, technology, mathematics and medicine (STEMM) employment in higher education and research. The Earlham Institute's (EI) first submission to the prestigious Athena SWAN Charter, owned and managed by the Equality Challenge Unit, has received the Bronze Award. SOCIAL MEDIA 184 Impressions 88,800

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

The Earlham Institute (EI) has been recognised in the annual HPCwire Readers' and Editors' Choice Awards for their high-performance computing bread wheat genome project, presented at the leading supercomputing event SC16 in Salt Lake City, Utah.

Article to highlight EI's research impact - With our cutting-edge technological capacity encompassing genome sequencing and analysis, the work we do is underpinned by open data, open publication and open-source software, which keeps us at the forefront of genomics research. SOCIAL MEDIA 39 Impressions 52,600

European Research Council awards €1.5M to arm cereals against pathogens and diseases

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Dr Ksenia Krasileva, Group Leader at the Earlham Institute (EI) and The Sainsbury Laboratory (TSL) has been awarded a €1.5M European Research Council Starting Grant to investigate the immune system of our most important crops. SOCIAL MEDIA Engagement 70 Impressions 24,000

New Scientist Live is a festival of ideas and discovery, taking place at ExCeL London. Rooted in the biggest, best and most provocative science, New Scientist Live will touch on all areas of human life. The show will feature four immersive zones covering Brain & Body, Technology, Earth and Cosmos. For four days this September, New Scientist Live will be like no other place on earth.

Earlham Institute will be present in the technology section, showcasing what goes on behind the scenes in delivering the latest advances in bioscience - from massive supercomputing power to next-generation genome sequencing hardware. SOCIAL MEDIA Engagement 196,000 Impressions 209

A training / workshop on efficient networking for scientists of all levels (from PhD students to post-docs and project leaders) from across the Norwich Research Park. The workshop included a "theory" part that concentrated on why and how to network; an experience sharing part where a few speakers talked about their experiences of engaging in networking / building relationships and how this has benefited them followed by interactive networking session between the participants, speakers and hosts. Attended by 26 delegates, 100% of delegates rated the course as very good or excellent.The session included:? Value of engaging with industry and wider public - Katia Brumpton (TGAC)? Efficient networking - strategy, preparation, etiquette, follow up - Lucy Marks (Norfolk Network)? Experience Sharing / Invited Speakers - showcasing of success (or horror) stories from networking and engagement with industry -(invited speakers)? Q&A session -? Interactive Session - building networking skills and feedback - delivered by Lucy Marks (NN), Stuart Catchpole (TGAC), Katia Brumpton (TGAC) and with invited speakers? informal session (communications games and further networking)

Year(s) Of Engagement Activity

2016

Description

Fascination of plants day

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Schools

Results and Impact

A national day to celebrate plants, we helped to run an event along with JIC to encourage young people into learning more about plants.

Year(s) Of Engagement Activity

2015

Description

Feature article on genomics in the Easton Daily Press

Form Of Engagement Activity

A magazine, newsletter or online publication

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Public/other audiences

Results and Impact

The Article was to cover the research activity at the Earlham Institute and at the Norwich Research park and how it would impact the general public

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Press release - Computational biologists have looked at the complex networks of interacting proteins that drive cancer formation, and found that targeting the neighbours of cancer-causing proteins may be just as effective as focusing on the cancer proteins themselves. SOCIAL MEDIA Engagement 93 Impressions 95170

Article to promoteThinking of learning a second language? Coding might be your best bet. The world of computing, rather than being dull and overly-complicated, is like learning how to compose a beautiful symphony but instead of writing notes, you write code.SOCIAL MEDIA Engagement 212 Impressions 105,000

Forming a second line of plant defence - capturing disease-resistant DNA

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Scientists have developed a new improved method for capturing longer DNA fragments, doubling the size up to 7000 DNA bases that can be analysed for novel genes which provide plants with immunity to disease. SOCIAL MEDIA Engagement 140 Impressions 90,400

Several of our scientists gave an in depth insight into how big data and genomics can be integrated with biological sciences in order to answer a swathe of important questions in the life sciences.

Year(s) Of Engagement Activity

2014

Description

From funding to the future

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

The Institute Development Scheme (IDS), set up in late 2015, aimed to support research at EI in several ways: through promoting creative, innovative and novel research, fostering the development of interdisciplinary teams and increasing collaboration both among academics and with industry.

We report here on several important projects, which highlight the range of applications of our next-generation sequencing and bioinformatics capabilities. SOCIAL MEDIA Engagement 95 Impressions 79291

The ferret (Mustela putorius furo) models biological processes that are highly relevant to human disease and health research such as influenza, cystic fibrosis (CF) and asthma. Since CF is a multi-organ disorder, research using CF ferrets span a range of organs, thus the impact of research in this model is broad and allows for the analysis of early stages of the diseases.

The recently completed draft of the ferret genome has allowed us to look more closely into ferret domestication and examine the underpinning processes of domestication from the ancestral European Polecat (M. putorius). We have sequenced eight domestic ferrets genomes and will sequence samples from European Polecat. Beneficial genetic variants increase in frequency due to positive selection together with linked neutral variants resulting in genomic islands of reduced heterozygosity between populations. By examining fixation indexes and heterozygosity between wild and domestic ferrets we can find genomic regions that have undergone selective sweeps.

Using whole genome sequencing also allows us to leverage the ferret genome sequence to look into the genetic diversity and evolution of other species of wild Mustelidae. The current population of the endangered Black-footed Ferret (M. nigripes) from North America stems from only seven individuals. Using whole genome sequencing of Black-footed Ferrets from both before and after the population crash we will identify genetic diversity not present in the current population with a view to reintroducing it via genome editing technology.

About two million years ago, the ancestral species of modern day Steppe Polecats (M. eversmanni) from Asia entered North America via the Bering Land Bridge and speciated into what is now Black-footed Ferret. Using a reference-free unbiased kmer approach, we will examine how closely-related Steppe Polecat is to both Black-footed Ferret and its sister species the European Polecat.

Year(s) Of Engagement Activity

2015

Description

Genome 10K - vertebrate 'genomic zoo' to help protect our planet

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Press release to promote the Genome 10K conference to be held at EI 2017.The Genome 10K initiative, led by the University of California, Santa Cruz Genomics Institute, aims to understand how complex animal life evolved through changes in DNA and use this knowledge to become better stewards of the planet. SOCIAL MEDIA Engagement 169 Impressions 171,000

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

An international team of researchers has identified the genetic mutations which allowed microalgae (phytoplankton) from the Southern Ocean to adapt to extreme and highly variable climates - a step towards understanding how polar organisms are impacted by climate change. SOCIAL MEDIA Engagement 95 Impressions 122000

The presentation took place as part of a workshop organised in Bogota (Colombia) between UK and Colombia scientific Institutions. The audience was composed of UK and Colombia university lecturers, Colombian industry partners. The presentation helped raising the international profile of Wilfried Haerty, Federica Di Palma and of the Earlham Institute

Year(s) Of Engagement Activity

2017

Description

Genomics Workshop to Position Genome Campus as a case study of excellence in the East of England Life Sciences Audit

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Professional Practitioners

Results and Impact

I was invited to participate in the workshop to position the Genome Campus, Cambridge, as a case study of excellence in the East of England Life Sciences Audit. Outputs included to describe how the campus drives collaboration and innovation in this area; highlight existing projects, opportunities, things we need to keep being world-class, what are strengths and weaknesses, how Govt can help.

Year(s) Of Engagement Activity

2017

Description

Germinal project workshop

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Industry/Business

Results and Impact

Germinal is part of a project in the UK called 'New Zoo' linking zoos to universities. The project between Banham Zooand the UEA will be a Science Discovery Centre for Education themed around 'environmental responsibility' and aKnowledge Exchange HUB for Research located at Banham Zoo.The aim of the project is to build on existing work with Banham Zoo to establish a strategic relationship that will enable UEA science to be developed in collaboration with the zoo, and to use the zoo to promote the research of UEAand the wider Norwich Research Park to the 250,000 people who visit the attraction each year. It will also promote regional economic growth as it has the potential to increase visitor numbers to Banham Zoo and the wider region. The focus of the workshop was around how Banham could showcase research to the public within the envisaged facility. They also ran an innovative think-tank to consider interactivity with the science across the NRP.

Year(s) Of Engagement Activity

2014

Description

Give your time to inspire a young person

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Schools

Results and Impact

Our staff gave specific career talks to young people and answered their questions, showing how diverse careers in the sciences can be; not just working in a lab, but in purchasing, comms and more.

Purpose of the meeting: To discuss what steps are necessary to prepare for possible future revival of great auks including: 1. The preparation of a suitably high quality great auk genome sequence, 2. The necessity for an annotated sequence/structural information,3. Comparisons with razorbill genome,4. Genome editing techniques,5. Germ cell transfer techniques,6. (Much later) great auk release into the wild,7. Ethical and ecological considerations.

Proposed structure of the project: In order to maintain this project's independence, and because it is probably too speculative and risky for public funding, it is the intention that the project will be carried forward initially with private funding. If, following the June meeting, we decide to go ahead, then a charitable foundation may be established to run the project.

Year(s) Of Engagement Activity

2015

Description

Host Year in Industry Project

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Undergraduate students

Results and Impact

Tarang hosted a Year in Industry student who selected his project on the 'Genetic basis of adaptation to extreme environments: insights from the genome of soda tilapia (Alcolapia grahami)'. This project offered a great opportunity for an undergraduate student, Nicole Forrester, to learn about cutting edge wet- and dry- lab techniques associated with the study of an important model system for evolution, genetic diversity and aquaculture practices. Nicole found the whole experience very insightful and thoroughly enjoyed it, as such, she selected a simialr themed project for her PhD Thesis.

Year(s) Of Engagement Activity

2016

Description

Hosted sixth form students visit for two weeks

Form Of Engagement Activity

Participation in an open day or visit at my research institution

Part Of Official Scheme?

No

Geographic Reach

Local

Primary Audience

Schools

Results and Impact

For two weeks we hosted four sixth form students with the purpose of showing some of the research that we undertake at the institute, as well as basic training in bioinformatics. This was extremely useful for the students, exposing them to a research environment of which, one was thinking of pursuing a research career in the future. We gave several talks, wet-lab and dry-lan training sessions as well as hand-on in the field sampel collection.

Year(s) Of Engagement Activity

2017

Description

Hosting and Training of PhD students from Tanzania

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Postgraduate students

Results and Impact

We hosted three PhD students at Earlham Institute for up to one month - the visit helped to develop their understanding and technical ability in several key genomic areas; this includes DNA/RNA extraction protocols, library preparation protocols, sequencing technologies and subsequent bioinformatics data analysis techniques. All of this was beneficial for developing current and future aquaculture projects. Also, by undertaking a course on Population Variation Genetics hosted at Earlham Institute in May, the students felt better prepared to carry out RAD data analysis (as part of their PhD) as well as other associated techniques, like phylogenetic analysis.

Details:Names:Levinus LeonardChrister NyinondiRedempta Kajungiro

Institutions: University of Dar Es Salaam and University of Dodoma, Tanzania

Nuffield Research Programme student Sophie Kirkwood tells us what it was like to work at EI and how it has influenced her decision to embark upon a STEM career. SOCIAL MEDIA Engagement 79 Impressions 72931

Several of our staff participated in the initiative, which allowed teenagers to pose questions to scientists, who were voted for in an "I'm a Celebrity" style competition. Challenged with making science more simple, our scientists had to sell their work to children. One member of staff actually won (!), which came along with a £500 grant for PE.

David Johnson - in my team - gave a presentation on "Data Infrastructures to Foster Data Reuse" at a workshop on Integrating Large Data into Plant Science: From Big Data to Discovery hosted by GARnet (the UK network for Arabidopsis researchers) and Egenis (the Exeter Centre for the Study of the Life Sciences). The workshop was held at Dartington Hall in Devon, South West England, and was well attended by researchers from the plant and biological science community worldwide as well as representatives from industry from organisations such as Syngenta.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Dr Ksenia Krasileva, Group Leader at the Earlham Institute (EI) and Fellow at The Sainsbury Laboratory (TSL) in collaboration with her TSL colleagues, Professor Jonathan Jones and Dr Panagiotis Sarris, have surveyed immune genes across flowering plants to uncover the molecular 'traps' that plants use to detect pathogens. SOCIAL MEDIA Engagements 218 Impressions 78,500

Advances in next-generation sequencing (NGS) technologies and the subsequent reduction in cost have enabled the research community to sequence the genomes of many non-model organisms. Genome assemblies using next generation technologies such as Illumina show high quality nucleotide level information, but are fragmented due to the inability to retain contiguity. The absence of low-cost methods for creating high quality genome sequences from a wide range of organisms currently hampers the generation of de novo genomes for comparative genomic studies, and new methodologies and data types need to be tested to achieve this goal. We have integrated NGS with nano-channel genome mapping and developed the PCR-free Discovar Assembly BioNano Scaffolding (PDABS) pipeline to assemble cheap, contiguous and robust genomes.

Year(s) Of Engagement Activity

2016

Description

Inside Science Workshop

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Schools

Results and Impact

A workshop for college aged students interesting in pursuing a career in the life sciences beyond University. The event covered all aspects of life on the research park, with specific activities aimed at generating discussion around bioinformatics, including phylogenetics.

Year(s) Of Engagement Activity

2014,2015

Description

International Conference Oral Presentation: Discovery and visualisation of homologous genes and gene families using Galaxy

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The oral presentation at the International Plant and Animal Genomes Conference (San Diego, USA) conference was selected on abstract submission. The presentation was delivered in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute

The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tarang Metha, Luca Penso Dolfin, Tomasz Wrzesinski, Will Nash, Padhmanand Sudhakar, Wilfried Haerty, Tamas Korcsmaros, Federica Di Palma and of the Earlham Institute

Year(s) Of Engagement Activity

2017

Description

International Conference Poster: Binding sites within long non-coding RNAs discriminate between RNA- and transcription mediated mechanism.

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute

Year(s) Of Engagement Activity

2017

Description

International Conference poster presentation: Discovery and visualisation of homologous genes and gene families using Galaxy

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The poster presentation at the 18th The Bioinformatics Open Source Conference (BOSC), 25th Intelligent Systems for Molecular Biology (ISMB) and 16th European Conference on Computational Biology - ISMB/ECCB conference was selected on abstract submission. The poster was presented in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute

Year(s) Of Engagement Activity

2017

Description

Into the light - the power of optical HPC

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Article to highlight the collaboration between EI and Optalysys - EI and the HPC hardware provider Optalysys joined forces to introduce the ground-breaking optical processing device GENESYS to perform large-scale DNA sequence searches for crucial genomics research powered by just a mains supply, and aims to be one of the top 50 fastest processing devices in the world by 2017. SOCIAL MEDIA Engagement 65 Impressions 47,900

Invited seminar: Characterization of transcriptional complexity of Voltage Gated Calcium Channels in the human brain using Nanopore long read sequencing

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Professional Practitioners

Results and Impact

Invited seminar at the Division of Evolution & Genomic Sciences, University of Manchester. The audience was composed of group leaders, University lecturers, postdoctoral researchers, graduates and undergraduates students interested in RNA biology.

Year(s) Of Engagement Activity

2018

Description

Invited seminar: Comparative genomics of Australian marsupials: Expansion of gene families and signatures of selection following an ancient divergence

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

Invited seminar at University College Dublin presented by Will Nash. The audience was composed of University professors and Lecturers, postdoctoral researchers, graduates and undergraduates students. Outcomes: Increased the international profile of Will Nash and Wilfried Haerty and increased the international profile of the Earlham Institute

Invited seminar at the MRC Institute of Genetics and Molecular Medicine. The audience consisted group leaders, University professors, University Lectures, postdoctoral researchers, graduates and undergraduates students.

Invited seminar in the satellite meeting of The Americal Society for Human Genetics organised by Oxford Nanopore. The audience of the seminar was composed of industrial professionals, group leaders, university professors and lecturers, postdoctoral researchers, graduates and undergraduate students. The seminar allowed to raise the personal profile of Wilfried Haerty and to raise the profile of the Earlham Institute

Year(s) Of Engagement Activity

2017

Description

Invited speaker International Institution: Characterization of functional long non-coding RNAs and their expression in the developing human brain

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The presentation took place as the result of an invitation to present at the ICenter for Regenerative Therapies Dresden. The audience was composed of university lecturers, graduate and undergraduate students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute

The presentation took place as the result of an invitation to present at the Evolution, Genomes and Speciation Laboratory, CNRS, Gif sur Yvette, France. The audience was composed of university lecturers, graduate and undergraduate students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute

Year(s) Of Engagement Activity

2016

Description

Invited speaker International Institution: Expression of lncRNAs across the human lifespan

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The presentation took place as the result of an invitation to present at the Center for Genomic Regulation, Barcelona, Spain. The audience was composed of university lecturers, graduate and undergraduate students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute

Year(s) Of Engagement Activity

2016

Description

It's not all about the money: Community investment

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Earlham Institute supports the AAAS Community Engagement Fellows Program - where budding community managers benefit from a shared knowledge base and peer support to excel their careers and make inroads to the scientific research network. SOCIAL MEDIA Engagement 30 Impressions 61670

Algae are an exceptional bunch of organisms for many reasons: particularly, they are responsible for half of the photosynthesis that takes place on the planet - and because of that - the oxygen in every second breath we take. SOCIAL MEDIA Engagement 51 Impressions 63821

KAT, the K-mer Analysis Toolkit, developed at the Earlham Institute, represents a necessary step to ensure that this is the case - allowing bioinformaticians to work more efficiently and ultimately improve the quality of genome projects. SOCIAL MEDIA Engagements 212 Impressions 96,700

An international group of students who visit the research park on a yearly basis. These students are some of the brightest from around the world, interested in science in general. One such attendee I knew personally from her company that won the Google Award when she was just 14, highlighting the calibre of young people that this event welcomes.

Year(s) Of Engagement Activity

2015,2016

Description

Long non-coding RNAmazing: X marks the spot

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Joint article with researcher WIlfried Haeryt on long non coding RNA - We used to think that only 1% of the human genome had any use. Oh, how times change.

The more we delve into the treasure trove of genetic information present in diverse genomes, from humans and worms to Arabidopsis and wheat, the more we have come to appreciate the bounty of non-coding elements that lie within.

Among the buried treasure - that composes just a small percentage of a genome - lie long non-coding RNAs (lncRNA), some of which, far from being junk, can provide insights into important regulatory mechanisms across all domains of life. SOCIAL MEDIA Engagement 183 Impressions 77,300

Interview article - We interview Antonia Ford, postdoctoral researcher at EI and Bangor University, who tells us all about aquaculture - and how understanding the genomics of native and introduced Tilapia species in Tanzania can help aquaculture breeders in the future. SOCIAL MEDIA Engagement 152 Impressions 120,000

KEC team seminar on why impact is important, ways to maximise impact and how the KEC Office can help.Session included a talk from Liliya Serazetdinova of The Knowledge Transfer Network (KTN) proviiding nsight into the UK Agri-Tech Strategy, current funding landscape and latest funding opportunities from Innovate UK (including new Agri-Tech Catalyst Round), Newton Fund, BBSRC and Horizon 2020, as well as the role of KTN in driving UK innovation.

Year(s) Of Engagement Activity

2016

Description

Member of MinION Analysis and Reference Consortium (MARC)

Form Of Engagement Activity

A formal working group, expert panel or dialogue

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

MARC is a consortium of scientists who seek to work together to understand how to get the best out of nanopore technology and to collaborate on international experiments and publications. So far, we have published two papers together which seek to describe and evaluate MinION technology. We are now working on a third publication based on an experiment to sequence river water around the world using nanopore sequencing.

Year(s) Of Engagement Activity

2015,2016,2017,2018

Description

MinIONs, MAP and MARC: Nanotechnology developments

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Highlighting our work with the Minion Nanopore We're working with the latest in nanopore sequencing technology to push the boundaries of low-cost, portable genomics solutions. SOCIAL MEDIA Engagement 86 Impressions 76,100

Article - Honey bees are as vital to our food systems as the crops they pollinate; with a swathe of economically important plants relying directly on bees for propagation. A recent study published in Nature highlighted a novel potential threat to these key creatures: an iflaviurscommon to wasps, bees and varroa mites, featuring the work of Purnima Pachori of Earlham Institute's Platforms & Pipelines Group. SOCIAL MEDIA Engagements 109 Impressions 112,000

Workshop looking at opportunities and challenges in Tanzanian tilapia fisheries and aquaculture programme. Programme included: Biodiversity, endemism, and importance/potential of native species to fisheries and aquaculture; Aquaculture initiatives in Tanzania, impact of non-native species stocked in natural water bodies on native species; Tanzanian tilapia species identification and sample collection; The TilapiaMap project and use of smartphone application; Group discussions and feedback on training needs and provision in Tanzania; Tour of facilities at Sokoine University, description of on-going aquaculture projects.

Year(s) Of Engagement Activity

2017

Description

My obscure route into science: Graham Etherington

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Interview with Graham Etherington - We interview Graham Etherington of our Regulatory and Systems Genomics Group, who fills us in about his journey from the RAF to the Falklands and finally to EI - as well as his love for all things avian. SOCIAL MEDIA Engagements 171 Impressions 78,400

We interviewed Jim Lipscombe form our Platform's and pipelines group about his route into science. It's time for round two - and this week we feature Jim Lipscombe of our Platforms & Pipelines Group, who most certainly did not have a typical route into a science career.

Read on to discover Jim's range of former jobs (from pubs to roofs and vineyards), his love for next generation sequencing, naked mole rats, making lego robots to better communicate science, and more! SOCIAL MEDIA Engagement 228 Impressions 116,000

NERC GCRF Workshop Sustainable Development Goal Interactions: The role of environmental science

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Policymakers/politicians

Results and Impact

Federica Di Palma gave an elevator pitch talk is "Reclaiming land lost to violence for the security of Colombian economy and society".

Year(s) Of Engagement Activity

2017

Description

National Conference Poster Presentation: Evolutionary History and Domestication of the Ferret (Mustela putorius furo)

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Professional Practitioners

Results and Impact

The poster presented at the Genome Science conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the national profile of Graham Etherington, Wilfried Haerty, Federica Di Palma and of the Earlham Institute

Year(s) Of Engagement Activity

2016

Description

National Institutes of Bioscience Meeting talk

Form Of Engagement Activity

A formal working group, expert panel or dialogue

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Professional Practitioners

Results and Impact

Participation at the National Institutes of Bioscience Meeting giving a talk on "The Norwich Research Park: A systems biology approach to human Health"

Year(s) Of Engagement Activity

2015

Description

New Investigator Award to help arrest global cereals killer

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Dr Ksenia Krasileva, Group Leader at the Earlham Institute (EI) and The Sainsbury Laboratory (TSL), has been awarded a New Investigator award from the Biotechnology and Biological Sciences Research Council (BBSRC) to find and breed plants that can better fend off this disease, and potentially reduce the use of pesticides.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Scientists at the Earlham Institute (EI) and the John Innes Centre (JIC) have developed a free online tool that will help a global community of scientists understand more about important food crops. SOCIAL MEDIA Engagements 225 Impressions 111,000

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Press release to promote the sequencing of an apple from Newton's apple tree Scientists will connect two of the most important scientific theories of all time - the law of universal gravitation and the theory of evolution - by unravelling the genetic code of the apple which inspired Isaac Newton's greatest discovery 350 years ago this year. - Social - Engagement 167 Impressions 109,000

The benefits of the human genome project are clear for all to see. We have gained tremendous knowledge of the genetic basis of disease and can better predict whether we are susceptible to certain conditions - ushering us into a promising new era of personalised genomics for medicine and nutrition. SOCIAL MEDIA Engagement 146 Impressions139,000

We opened our doors to the Women's Institute of Norfolk, to whom we delivered a three part workshop during which they had lab tours, data centre tours and a DNA extraction workshop, hosted by many of our platforms and pipelines team.

Year(s) Of Engagement Activity

2015

Description

Norwich Science Park Open Day

Form Of Engagement Activity

Participation in an open day or visit at my research institution

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Public/other audiences

Results and Impact

Presented poster on work linked to Big Data Bioinformatics

Year(s) Of Engagement Activity

2016

Description

Nuffield plant science placements

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Schools

Results and Impact

Each year a number of Nuffield placement students come to the research park. Each year, we have given them an insight into what goes on at EI (TGAC), with tours and activities, as well as occasional placements.

Year(s) Of Engagement Activity

2015,2016,2017

Description

Of Mice and Men: life at the limits

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

How are mice so adaptable to extreme environments? We speak to EI Fellow David Thybert about the hardy desert mouse. SOCIAL MEDIA Engagement 76 Impressions 110,000

Open day at the institute, poster presentation on Evolution of tissue-specific regulatory programs in cichlids - engaging with the general public allowed for public awareness of our research and imapct, as well as sparking questions and general discussion surrounding the importance of this age of genomics research.

Year(s) Of Engagement Activity

2015

Description

Open Lecture for the School of Biology at the University of East Anglia

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

Local

Primary Audience

Undergraduate students

Results and Impact

I gave an open lecture, followed by questions and 1:1 meetings with faculty and students at the UEA

Year(s) Of Engagement Activity

2015

Description

Open data sharing: how and why?

Form Of Engagement Activity

Engagement focused website, blog or social media channel

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Blog post on open data sharing The more open biological data is, and the better it is shared, the more we can hope to get out of it for the benefit of all. SOCIAL MEDIA Engagement 15 Impressions 17801

Opportunities and challenges in Tanzanian tilapia fisheries and aquaculture programme

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Other audiences

Results and Impact

Workshop 1: Biodiversity, species identification, and stocking of non-native tilapiines, Sokoine University of Agriculture, Morogoro, Tanzania, 16-17 Jan 2017. This workshop raised awareness of potential threats to native Tanzanian Tilapia species by breeding and stocking non-native species in Tanzanian water bodies. We included practical training in the identification of tilapia species, both in the field and from captive breeding facilities, through introduction of the new smartphone app 'TilapiaMap', and featured research seminars addressing issues of hybridisation, and the problems that mixed stocks may present to aquaculture.

Year(s) Of Engagement Activity

2017

Description

Oral Presentation - Norwich Science Festival

Form Of Engagement Activity

A talk or presentation

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Public/other audiences

Results and Impact

Around 40 people attended a talk given on "Food for thought" - understanding biodiversity and it's impact on life and health; this sparked extensive questions and discussion afterwards. As a result, the event reported great interest in the area of biodiversity, fish biology and aquaculture (fish-farming).

Oral presentation at international conference: Characterization of functional long non-coding RNAs in human

Form Of Engagement Activity

Participation in an activity, workshop or similar

Part Of Official Scheme?

No

Geographic Reach

International

Primary Audience

Professional Practitioners

Results and Impact

The presentation at the Genome 10K / Genome Science conference was selected on abstract submission. The presentation was delivered in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute

Year(s) Of Engagement Activity

2017

Description

Our Director of Science honoured for Biological and Medical Sciences

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Other audiences

Results and Impact

Director of Science Dr Federica Di Palma is awarded two honorary professorships by the University of East Anglia (UEA) for the School of Biological Sciences and Norwich Medical School. SOCIAL MEDIA Engagement 132 Impressions 33,400

2017 has swung in with full force and springtime is now just around the corner. We thought we'd look back on which of our articles, features and news stories were most popular in 2016. SOCIAL MEDIA Engagement 97 Impressions 80005

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

The Genome Analysis Centre (TGAC), with partners in the UK, Colombia and Kenya bring together their leading expertise in forage breeding for animal nutrition, cutting-edge genomics and phenomics technologies, to accelerate the improvement of Brachiaria, a vital livestock forage crop in central Africa and Latin America.

Year(s) Of Engagement Activity

2015

Description

PRESS RELEASE: An integrated approach combining genomics, genetics and agronomy to improve the European wheat and barley production

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

An integrated approach combining genomics, genetics and agronomy to improve the European wheat and barley production

PRESS RELEASE: Chair of TGAC's Scientific Advisory Board elected to the Fellowship of the Academy of Medical Sciences

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

Chair of TGAC's Scientific Advisory Board elected to the Fellowship of the Academy of Medical Sciences

Year(s) Of Engagement Activity

2015

Description

PRESS RELEASE: Changing the biological data visualisation world

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

Scientists at TGAC, alongside European partners, have created a cutting-edge, open source community for the life sciences. BioJavaScript (BioJS) is a free, accessible software library that develops visualisation tools for different types of biological data. Data visualisation allows researchers to present their data to communicate key scientific hypotheses and concepts to a wider audience. Helping us to understand complex biological systems in relation to improving plant, animal and human health.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

Contribution to wheat genome in spotlight at supercomputing conference

Year(s) Of Engagement Activity

2014

Description

PRESS RELEASE: Crowd-sourcing the E. coli

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

Crowd-sourcing the E. coli

Year(s) Of Engagement Activity

2011

Description

PRESS RELEASE: DNA Synthesis at the Norwich Research Park

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

The Genome Analysis Centre (TGAC) has been awarded £1.9M to establish a DNA synthesis facility at the Norwich Research Park (NRP). TGAC has been selected as one of only five centres across the UK to develop a state-of-the-art DNA synthesis centre in Norwich. The facility aims to support the design, generation and exploitation of high-value compounds and bioactives obtained from plants and microbes to contribute to areas of strength within the NRP. Recent advances in DNA technologies have stimulated the development of innovative research in synthetic biology. The investment announced today will equip the NRP with the cutting-edge technology in DNA synthesis that will build on the existing National Capability in Genomics at TGAC and help to propel the UK to the forefront of synthetic biology research.

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

National

Primary Audience

Media (as a channel to the public)

Results and Impact

Vicky Schneider, 361° Division (Training, Public Engagement, Best Practice & e-Science) at The Genome Analysis Centre TGAC, along with UK and European partners, has reviewed key aspects of standards and formats of biological data to highlight the importance of data integration and management tools for biologists.

Year(s) Of Engagement Activity

2015

Description

PRESS RELEASE: Deputy PM visits TGAC as part of City Deal signed at Norwich Research Park

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview

Part Of Official Scheme?

No

Geographic Reach

Regional

Primary Audience

Media (as a channel to the public)

Results and Impact

Deputy PM visits TGAC as part of City Deal signed at Norwich Research Park

Year(s) Of Engagement Activity

2013

Description

PRESS RELEASE: Discovering the decoding of living systems

Form Of Engagement Activity

A press release, press conference or response to a media enquiry/interview